CITY Comptroller Bill Thompson has been a busy guy lately, addressing the city’s fiscal crisis – but not too busy to get married. Thompson and his honey of two years, Harvard Law School alum and Museum for African Art President Elsie McCabe, quietly tied the knot in front of a few family members at a Brooklyn church a few days ago. The newlyweds have yet to select a honeymoon spot, but pals said when they do finally get away, McCabe’s 11-year-old twins won’t be coming with them. Thompson declined to comment.